The N–K ionisation energies of cytidine are differentiated by the amino nitrogen (–N–) and imino nitrogen (–N=) sites, rather than by their locations in or out of the pyrimidine ring. The present density functional theory calculations assign the lower-binding energy peak of the X-ray spectroscopic experiment to be the imino N–K site of N(3)a, whereas the amino N–K sites of N(1)a and N(8)a exhibit blue shift so that they both contribute to the higher energy peak in the binding energy spectra.